Structure of PDB 8pvk Chain CH Binding Site BS03

Receptor Information
>8pvk Chain CH (length=627) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGWKDIPPVPTAQEFIDIVLSRTQRRLPTQIRPGFKISRIRAFYTRKVKF
TQETCSEKFGAIISSFPVLSDQHPFHRDLMNILYDADHFKVALGQISTAK
NLIETISRDYVRLLKYAQSLYQCKQLKRAALGRMATLIKRLKDPLIYLDQ
VRQHLARLPDINPTTRTLLVAGFPNVGKSSFVRSVTRADTPVEPYAFTTK
SLFVGHLDYKYLRYQVIDTPGILDHPLEEMNTIEMQSVTALAHLRAAVLY
FMDISEQCGFSLKAQINLFKSIKPLFANKMVFIVLNKMDIKKFEELDPEM
QQEINDLTKSGEVEILRASCATQEGVQEVKNHVCERLLVERVSQKLKAGT
HSNGNIGTRLQEVMARIHVATPMDGTTRETFIPEAVKNLKKYDKNDPNRR
VLARDIEEANGGAGVFNVDLRKDWILENPEWKYDKIPEIFDGKNVYDYID
PDIDAKLQALEEEEERLEKEGFYDEDDEEEEEILQKAEYIREQHALIRNE
AKMRKSLKNRAIIPRKAVKKPLSQLEDHLDQLGVDTEAIGLRARAQTSAK
ERLARSRSRARSVAATNRLQDGVQGTTLRSKAERQAKLAQRKMNRMARQG
EADRHIHASMPKHLFSGKRTIGKTDRR
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8pvk Chain CH Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8pvk Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		N176 G178 K179 S180 S181 V193 T200 D219 K288 D290 I291 S320 C321 A322
Binding residue
(residue number reindexed from 1)		N175 G177 K178 S179 S180 V192 T199 D218 K287 D289 I290 S319 C320 A321
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0046872 metal ion binding
Biological Process
GO:0042254 ribosome biogenesis
GO:0042273 ribosomal large subunit biogenesis
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8pvk, PDBe:8pvk, PDBj:8pvk
PDBsum8pvk
PubMed37921038
UniProtG0S8F1|NOG1_CHATD Nucleolar GTP-binding protein 1 (Gene Name=NOG1)

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